November 2013 issue
4th International Symposium on Diffraction Structural Biology (ISDSB2013)
Fukiage Hall, Nagoya, Japan, 26-29 May 2013
diffraction structural biology
The development of a high-duty-cycle microsecond time-resolution SAXS capability at the Biophysics Collaborative Access Team beamline (BioCAT) 18ID at the Advanced Photon Source, Argonne National Laboratory, USA, is reported.
The viral and virus-related structures of Rice dwarf virus have been visualized by cryo-electron microscopy and tomography revealing the viral infection and replication mechanisms.
A new type of U-shape anti-cathode X-ray generator in which the inner surface of a cylindrical target is irradiated by an electron beam has been made by modifying a conventional rotating anti-cathode X-ray generator whose brightness in the catalog is 12 kW mm−2. A brightness of 129 kW mm−2 was thereby obtained with this new U-shape-type X-ray generator. This new X-ray generator is expected to be of keen interest for applications in academia, industry and in hospitals.
The neutron crystal structure of human transthyretin is presented.
The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described.
Shortfin mako shark haemoglobin adopts an unliganded deoxy T state conformation, which is shown from the quaternary structural features, interface interactions and heme binding sites of different subunits of haemoglobin with high-resolution X-ray data.
A contrast enhancement approach utilizing a new type of mathematical morphology called rotational morphological processing is introduced. The method is quantitatively evaluated and then applied to some medical images.
Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution.
The crystallization-phase-diagram-guided method is effective for growing large protein crystals for neutron protein crystallography.
Various structural fluctuations of phosphate groups and hydration in the minor groove were observed in the crystal structure of Z-DNA in the absence of divalent metal cations and polyamines.
Wide-angle X-ray scattering data using a third-generation synchrotron radiation source are presented.
X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis.
Archiving of raw diffraction images data has led to new structural chemistry information being obtained for previously published results, which leads to the conclusion that carboplatin has partially converted to cisplatin in the high NaCl concentration conditions used in the crystallization procedure.
The crystal structure of endo-1,4-β-glucanase from the earthworm Eisenia fetida, which retained sufficient cellulase activity at low temperature, was determined at 1.5 Å resolution.
A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed.
The anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea (Ct3GT-A) was expressed in Escherichia coli, and the three-dimensional structure of Ct3GT-A was determined using X-ray crystallography. This report describes the architecture of Ct3GT-A, including the structures of the donor- and acceptor-binding sites.
A code with an algorithm for high-speed classification of X-ray diffraction patterns has been developed. Results obtained for a set of 1 × 106 simulated diffraction patterns are also reported.
The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a β-sheet which is a common structure in CDK2–ligand complexes. Here, the reason why TEI-I01800 does not become a strong inhibitor against CDK2 based on the conformation of TEI-I01800 is presented.
SPring-8 BL41XU provides a high-flux X-ray beam of size 10–50 µm, and enables high-quality diffraction data to be obtained from various types of protein crystals. Details of this beamline and an upgrade project are described.
The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The present study shows that the benzimidazole ring of the inhibitor takes the stable stacking interaction with the protonated His57 in the catalytic domain of human chymase.
The present study analysed small-angle X-ray scattering profiles of myoglobin to examine how removal of the heme changes the intermolecular interaction.
The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate.
A docking study of Mtb Eis with its substrate DUSP16/MKP-7 was performed. The docking model suggests dissociation of hexameric Mtb Eis into dimers or monomers.
According to the structural and biochemical analysis of the stomatin-specific protease 1510-N, two degraded products were produced via acyl-enzyme intermediates. The N-terminal half of the substrate peptide binds to 1510-N more tightly than the C-terminal half of the peptide.
The BL-17A macromolecular crystallography beamline at the Photon Factory was updated to improve the accuracy of diffraction experiments conducted using tiny crystals.
1/2SLPI is a C-terminal domain of SLPI (secretory leukocyte protease inhibitor) which inhibits various serine proteases broadly. The present study is the first X-ray structural report on how 1/2SLPI with P1 Leu strongly inhibits trypsin and how it can inhibit multiple serine proteases.
An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported.
An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry.
Fundamental trials to realise the proton polarization technique for detecting hydrogen with higher sensitivity in neutron protein crystallography are described.
The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD+ glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules.
The Japan Aerospace Exploration Agency's `high-quality protein crystal growth' project is introduced. If crystallization conditions were carefully fixed in ground-based experiments, high-quality protein crystals grew in microgravity in many experiments on the International Space Station, especially when a highly homogeneous protein sample and a viscous crystallization solution were employed.
The high-resolution crystal structure of the human CK2 catalytic subunit reveals the structural insights that probably promote drug discovery.
Protein unfolding at an air–water interface is followed in real time by a recently developed simultaneous multiple-angle–wavelength-dispersive X-ray reflectometer with a time resolution of 1 s.
The crystal structure of EcoMinCNTD dimerized via domain swapping was solved at 2.3 Å resolution. The present study suggests that EcoMinC dimerizes through both EcoMinCNTD and EcoMinCCTD.
Using the high-pressure cryocooling method, the high-resolution X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. This is the first ultra-high-resolution structure obtained from a high-pressure cryocooled crystal.
The time-of-flight neutron single-crystal diffractometer iBIX at the next-generation neutron source J-PARC has been upgraded and is available for user experiments on protein samples in particular. Neutron structure analysis of a standard protein sample was carried out in order to evaluate the performance of iBIX.
A convenient gas-derivatization tool for protein crystals is presented in combination with a fine-needle capillary and a gas-pressure regulator.
Numerical analysis of the concentration depletion zones in a transient state suggested that, in microgravity, protein crystals grow in a lower supersaturation and the impurity ratio decreases in the centre of the crystal.